PXD031984

PXD031984 is an original dataset announced via ProteomeXchange.

Title	Single-copy locus isolation identifies distinct proteomes of early- and late-firing DNA replication origin chromatin
Description	The chromatin at origins of replication is the template for DNA replication initiation in eukaryotic genomes. However, whether the chromatin composition instructs individual origins to fire early-efficiently (EE) or late-inefficiently (LI) remains to be investigated. Here, we used site-specific recombination and a single-locus chromatin isolation approach to purify selected EE and LI replication origins from chromosome III of Saccharomyces cerevisiae. Using mass spectrometry, we define the histone modification landscape and identify the protein composition of defined ~1kb native chromatin regions surrounding the EE and LI replication start sites. We confirm expected origin interactors but also find unexpected interactions, such as the Ask1 subunit of the kinetochore-associated DASH complex. Strikingly, we show that Ask1 is a critical factor in the replication timing control of specific origins in yeast. These results highlight that our unbiased approach can specifically identify the functionally-relevant proteome at a single-copy locus of interest and provide a detailed view of histone modification and protein interaction networks on replication origin chromatin. The current dataset contains proteomic data used for the histone PTM analysis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:45:26.070.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrey Tvardovskiy
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monomethylated residue; acetylated residue; dimethylated residue; N6,N6,N6-trimethyl-L-lysine
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-02 01:10:39	ID requested
1	2024-10-07 13:45:35	announced
⏵ 2	2024-10-22 05:45:28	announced	2024-10-22: Updated project metadata.

10.1016/j.celrep.2023.112045;

Wei, β M, Chanou A, Schauer T, Tvardovskiy A, Meiser S, K, ö, nig AC, Schmidt T, Kruse E, Ummethum H, Trauner M, Werner M, Lalonde M, Hauck SM, Scialdone A, Hamperl S, Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control. Cell Rep, 42(2):112045(2023) [pubmed]

submitter keyword: replication timing, replication efficiency, Affinity purification,Locus-specific chromatin isolation, DNA replication origin, histone PTMs, Site-specific recombination

Stephan Hamperl
contact affiliation	Chromosome dynamics and genome stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany
contact email	stephan.hamperl@helmholtz-muenchen.de
lab head
Andrey Tvardovskiy
contact affiliation	Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
contact email	andrey.tvardovskiy@helmholtz-muenchen.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/05/PXD031984

PRIDE project URI

• PRIDE
  1. PXD031984
     1. Label: PRIDE project
     2. Name: Single-copy locus isolation identifies distinct proteomes of early- and late-firing DNA replication origin chromatin